The PENGUIN approach to reconstruct protein interactions at enhancer-promoter regions and its application to prostate cancer

Alexandros Armaos, François Serra, Iker Núñez-Carpintero, Ji-Heui Seo, Sylvan C. Baca, Stefano Gustincich, Alfonso Valencia, Matthew L. Freedman, Davide Cirillo (), Claudia Giambartolomei () and Gian Gaetano Tartaglia ()
Additional contact information
Alexandros Armaos: Istituto Italiano di Tecnologia, CHT@Erzelli
François Serra: Barcelona Supercomputing Center
Iker Núñez-Carpintero: Barcelona Supercomputing Center
Ji-Heui Seo: Dana Farber Cancer Institute
Sylvan C. Baca: Dana Farber Cancer Institute
Stefano Gustincich: Istituto Italiano di Tecnologia, CHT@Erzelli
Alfonso Valencia: Barcelona Supercomputing Center
Matthew L. Freedman: Dana Farber Cancer Institute
Davide Cirillo: Barcelona Supercomputing Center
Claudia Giambartolomei: Istituto Italiano di Tecnologia, CHT@Erzelli
Gian Gaetano Tartaglia: Istituto Italiano di Tecnologia, CHT@Erzelli

Nature Communications, 2023, vol. 14, issue 1, 1-17

Abstract: Abstract We introduce Promoter-Enhancer-Guided Interaction Networks (PENGUIN), a method for studying protein-protein interaction (PPI) networks within enhancer-promoter interactions. PENGUIN integrates H3K27ac-HiChIP data with tissue-specific PPIs to define enhancer-promoter PPI networks (EPINs). We validated PENGUIN using cancer (LNCaP) and benign (LHSAR) prostate cell lines. Our analysis detected EPIN clusters enriched with the architectural protein CTCF, a regulator of enhancer-promoter interactions. CTCF presence was coupled with the prevalence of prostate cancer (PrCa) single nucleotide polymorphisms (SNPs) within the same EPIN clusters, suggesting functional implications in PrCa. Within the EPINs displaying enrichments in both CTCF and PrCa SNPs, we also show enrichment in oncogenes. We substantiated our identified SNPs through CRISPR/Cas9 knockout and RNAi screens experiments. Here we show that PENGUIN provides insights into the intricate interplay between enhancer-promoter interactions and PPI networks, which are crucial for identifying key genes and potential intervention targets. A dedicated server is available at https://penguin.life.bsc.es/ .

Date: 2023
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DOI: 10.1038/s41467-023-43767-1

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